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INTACT method for gene expression and chromatin profiling of individual cell types within a tissue

ABSTRACT: We used in vivo biotin labeling of a nuclear envelope protein in individual cell types followed by affinity isolation of labeled nuclei to measure gene expression and chromatin features of the hair and non-hair cell types of the Arabidopsis root epidermis. Keywords: Chromatin affinity-purification on microarray All experiments were done using two channels per chip. Two types of experiments were performed. Expression profiling was performed by comparing cDNAs synthesized from nuclear RNA isolated from INTACT-prepared Arabidopsis nuclei to total sonicated genomic DNA isolated from Arabidopsis plants. Chromatin profiling was performed using INTACT-prepared Arabidopsis nuclei. DNA isolated by Chromatin immunoprecipitation (ChIP) using antibodies to modified histones was compared to histone H3 ChIP DNA from the same sample.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Jorja Henikoff

PROVIDER: E-GEOD-19654 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A simple method for gene expression and chromatin profiling of individual cell types within a tissue.

Deal Roger B RB Henikoff Steven S

Developmental cell 20100601 6

Understanding the production and function of specialized cells during development requires the isolation of individual cell types for analysis, but this is currently a major technical challenge. Here we describe a method for cell type-specific RNA and chromatin profiling that circumvents many of the limitations of current methods for cell isolation. We used in vivo biotin labeling of a nuclear envelope protein in individual cell types followed by affinity isolation of labeled nuclei to measure g ...[more]

PMID: 20627084

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